› 8bip

Electron Microscopy
3.1Å resolution

Structure of a yeast 80S ribosome-bound N-Acetyltransferase B complex

Released:
DOI: 10.2210/pdb8bip/pdb
PDB entry 8bip coloured by chain, front view.
PDB entry 8bip coloured by chain, side view.
PDB entry 8bip coloured by chain, top view.
Source organism: Saccharomyces cerevisiae
Primary publication:
The dynamic architecture of Map1- and NatB-ribosome complexes coordinates the sequential modifications of nascent polypeptide chains.
Knorr AG, Mackens-Kiani T, Musial J, Berninghausen O, Becker T, Beatrix B, Beckmann R
OpenAccess logo PLoS Biol 21 e3001995 (2023)
PMID: 37079644
Related structures: EMD-16086

Function and Biology Details

Reaction catalysed: 
Acetyl-CoA + an N-terminal L-methionyl-L-asparaginyl-[protein] = an N-terminal N(alpha)-acetyl-L-methionyl-L-asparginyl-[protein] + CoA
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 47-mer (preferred)
PDBe Complex ID:
PDB-CPX-272126 (preferred)
Entry contents:
44 distinct polypeptide molecules
3 distinct RNA molecules
Macromolecules (47 distinct):
Large ribosomal subunit protein uL2A Chain: LA
Molecule details ›
Chain: LA
Length: 251 amino acids
Theoretical weight: 27.09 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P0CX45 (Residues: 2-252; Coverage: 99%)
Gene names: RPL2A, RPL5B, YFR031BC, YFR031C-A
Sequence domains:
Large ribosomal subunit protein uL3 Chain: LB
Molecule details ›
Chain: LB
Length: 386 amino acids
Theoretical weight: 43.72 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P14126 (Residues: 2-387; Coverage: 100%)
Gene names: MAK8, RPL3, TCM1, YOR063W, YOR29-14
Sequence domains: Ribosomal protein L3
Large ribosomal subunit protein uL4A Chain: LC
Molecule details ›
Chain: LC
Length: 361 amino acids
Theoretical weight: 39.03 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P10664 (Residues: 2-362; Coverage: 100%)
Gene names: RPL2, RPL2A, RPL4A, YBR0315, YBR031W
Sequence domains:
Large ribosomal subunit protein uL18 Chain: LD
Molecule details ›
Chain: LD
Length: 294 amino acids
Theoretical weight: 33.42 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P26321 (Residues: 4-297; Coverage: 99%)
Gene names: LPI14W, RPL1, RPL1A, RPL5, YPL131W
Sequence domains:
Large ribosomal subunit protein eL6B Chain: LE
Molecule details ›
Chain: LE
Length: 175 amino acids
Theoretical weight: 19.88 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P05739 (Residues: 2-176; Coverage: 99%)
Gene names: L9324.4, RPL16B, RPL17B, RPL6B, YL16B, YLR448W
Sequence domains: Ribosomal protein L6e
Large ribosomal subunit protein uL30A Chain: LF
Molecule details ›
Chain: LF
Length: 222 amino acids
Theoretical weight: 25.24 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P05737 (Residues: 23-244; Coverage: 91%)
Gene names: RPL6A, RPL7A, RPL8A, YGL076C, YL8A
Sequence domains:
Large ribosomal subunit protein eL8A Chain: LG
Molecule details ›
Chain: LG
Length: 233 amino acids
Theoretical weight: 25.81 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P17076 (Residues: 24-256; Coverage: 91%)
Gene names: MAK7, RPL4A, RPL8A, YHL033C
Sequence domains: Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
Large ribosomal subunit protein uL6A Chain: LH
Molecule details ›
Chain: LH
Length: 191 amino acids
Theoretical weight: 21.61 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P05738 (Residues: 1-191; Coverage: 100%)
Gene names: RPL8A, RPL9, RPL9A, YGL147C
Sequence domains: Ribosomal protein L6
Large ribosomal subunit protein uL16 Chain: LI
Molecule details ›
Chain: LI
Length: 218 amino acids
Theoretical weight: 25.08 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P41805 (Residues: 2-219; Coverage: 99%)
Gene names: GRC5, QSR1, RPL10, YLR075W
Sequence domains: Ribosomal protein L16p/L10e
Large ribosomal subunit protein uL5B Chain: LJ
Molecule details ›
Chain: LJ
Length: 169 amino acids
Theoretical weight: 19.27 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q3E757 (Residues: 6-174; Coverage: 97%)
Gene names: RP39B, RPL11B, RPL16B, YGR085C
Sequence domains:
Large ribosomal subunit protein eL13A Chain: LL
Molecule details ›
Chain: LL
Length: 193 amino acids
Theoretical weight: 21.89 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q12690 (Residues: 2-194; Coverage: 97%)
Gene names: RPL13A, YDL082W
Sequence domains: Ribosomal protein L13e
Large ribosomal subunit protein eL14A Chain: LM
Molecule details ›
Chain: LM
Length: 136 amino acids
Theoretical weight: 14.98 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P36105 (Residues: 3-138; Coverage: 99%)
Gene names: RPL14A, YKL006W, YKL153
Sequence domains:
Large ribosomal subunit protein eL15A Chain: LN
Molecule details ›
Chain: LN
Length: 203 amino acids
Theoretical weight: 24.35 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P05748 (Residues: 2-204; Coverage: 100%)
Gene names: RPL10A, RPL13A, RPL15A, YL10A, YLR029C
Sequence domains: Ribosomal L15
Large ribosomal subunit protein uL13A Chain: LO
Molecule details ›
Chain: LO
Length: 197 amino acids
Theoretical weight: 22.03 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P26784 (Residues: 3-199; Coverage: 99%)
Gene names: RPL13, RPL16A, RPL21A, YIL133C
Sequence domains: Ribosomal protein L13
Large ribosomal subunit protein uL22A Chain: LP
Molecule details ›
Chain: LP
Length: 183 amino acids
Theoretical weight: 20.46 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P05740 (Residues: 2-184; Coverage: 100%)
Gene names: RPL17, RPL17A, RPL20A, YKL180W
Sequence domains: Ribosomal protein L22p/L17e
Large ribosomal subunit protein eL18A Chain: LQ
Molecule details ›
Chain: LQ
Length: 185 amino acids
Theoretical weight: 20.48 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P0CX49 (Residues: 2-186; Coverage: 100%)
Gene names: RP28A, RPL18A, YOL120C
Sequence domains: Ribosomal protein 60S L18 and 50S L18e
Large ribosomal subunit protein eL19A Chain: LR
Molecule details ›
Chain: LR
Length: 188 amino acids
Theoretical weight: 21.63 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P0CX82 (Residues: 2-189; Coverage: 100%)
Gene names: RPL19A, RPL23A, YBR084BC, YBR084C-A, YL14A
Sequence domains: Ribosomal protein L19e
Large ribosomal subunit protein eL20A Chain: LS
Molecule details ›
Chain: LS
Length: 171 amino acids
Theoretical weight: 20.35 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P0CX23 (Residues: 2-172; Coverage: 99%)
Gene names: RPL18A, RPL18A2, RPL20A, YM9408.04C, YMR242C
Sequence domains: Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A
Large ribosomal subunit protein eL21A Chain: LT
Molecule details ›
Chain: LT
Length: 159 amino acids
Theoretical weight: 18.15 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q02753 (Residues: 2-160; Coverage: 99%)
Gene names: RPL21A, URP1, YBR1401, YBR191W
Sequence domains: Ribosomal protein L21e
Large ribosomal subunit protein eL22A Chain: LU
Molecule details ›
Chain: LU
Length: 100 amino acids
Theoretical weight: 11.26 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P05749 (Residues: 9-108; Coverage: 83%)
Gene names: L2168, RPL22A, YLR061W
Sequence domains: Ribosomal L22e protein family
Large ribosomal subunit protein uL14A Chain: LV
Molecule details ›
Chain: LV
Length: 136 amino acids
Theoretical weight: 14.36 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P0CX41 (Residues: 2-137; Coverage: 99%)
Gene names: RPL17A, RPL17AA, RPL23A, YBL0713, YBL087C
Sequence domains: Ribosomal protein L14p/L23e
Large ribosomal subunit protein eL24A Chain: LW
Molecule details ›
Chain: LW
Length: 126 amino acids
Theoretical weight: 14.62 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P04449 (Residues: 1-126; Coverage: 81%)
Gene names: RP29, RPL24A, RPL30A, YGL031C
Sequence domains: Ribosomal protein L24e
Large ribosomal subunit protein uL23 Chain: LX
Molecule details ›
Chain: LX
Length: 121 amino acids
Theoretical weight: 13.77 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P04456 (Residues: 22-142; Coverage: 85%)
Gene names: RPL25, YOL127W
Sequence domains:
Large ribosomal subunit protein uL24A Chain: LY
Molecule details ›
Chain: LY
Length: 125 amino acids
Theoretical weight: 14.01 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P05743 (Residues: 2-126; Coverage: 98%)
Gene names: L8300.4, RPL26, RPL26A, RPL33A, YLR344W
Sequence domains:
Large ribosomal subunit protein eL27A Chain: LZ
Molecule details ›
Chain: LZ
Length: 135 amino acids
Theoretical weight: 15.44 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P0C2H6 (Residues: 2-136; Coverage: 99%)
Gene names: RPL27, RPL27A, YHR010W
Sequence domains: Ribosomal L27e protein family
Large ribosomal subunit protein uL15 Chain: La
Molecule details ›
Chain: La
Length: 148 amino acids
Theoretical weight: 16.63 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P02406 (Residues: 2-149; Coverage: 99%)
Gene names: CYH2, RPL28, YGL103W
Sequence domains: Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
Large ribosomal subunit protein eL29 Chain: Lb
Molecule details ›
Chain: Lb
Length: 58 amino acids
Theoretical weight: 6.56 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P05747 (Residues: 2-59; Coverage: 98%)
Gene names: RPL29, YFR032BW, YFR032C-A, YL43
Sequence domains: Ribosomal L29e protein family
Large ribosomal subunit protein eL30 Chain: Lc
Molecule details ›
Chain: Lc
Length: 96 amino acids
Theoretical weight: 10.49 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P14120 (Residues: 9-104; Coverage: 91%)
Gene names: RPL30, RPL32, YGL030W
Sequence domains: Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
Large ribosomal subunit protein eL31A Chain: Ld
Molecule details ›
Chain: Ld
Length: 109 amino acids
Theoretical weight: 12.65 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P0C2H8 (Residues: 4-112; Coverage: 97%)
Gene names: D2478, RPL31A, RPL34, RPL34A, YDL075W
Sequence domains: Ribosomal protein L31e
Large ribosomal subunit protein eL32 Chain: Le
Molecule details ›
Chain: Le
Length: 127 amino acids
Theoretical weight: 14.48 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P38061 (Residues: 2-128; Coverage: 98%)
Gene names: RPL32, YBL0838, YBL092W
Sequence domains: Ribosomal protein L32
Large ribosomal subunit protein eL33A Chain: Lf
Molecule details ›
Chain: Lf
Length: 106 amino acids
Theoretical weight: 12.05 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P05744 (Residues: 2-107; Coverage: 99%)
Gene names: LPI4W, P2625, RPL33A, RPL37A, YPL143W
Sequence domains: Ribosomal protein L35Ae
Large ribosomal subunit protein eL34A Chain: Lg
Molecule details ›
Chain: Lg
Length: 112 amino acids
Theoretical weight: 12.61 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P87262 (Residues: 2-113; Coverage: 93%)
Gene names: RPL34A, YER056BC, YER056C-A
Sequence domains: Ribosomal protein L34e
Large ribosomal subunit protein uL29A Chain: Lh
Molecule details ›
Chain: Lh
Length: 119 amino acids
Theoretical weight: 13.81 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P0CX84 (Residues: 2-120; Coverage: 99%)
Gene names: D1249, RPL35A, SOS1, YDL191W
Sequence domains: Ribosomal L29 protein
Large ribosomal subunit protein eL36A Chain: Li
Molecule details ›
Chain: Li
Length: 99 amino acids
Theoretical weight: 11.02 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P05745 (Residues: 2-100; Coverage: 99%)
Gene names: RPL36A, RPL39A, YM9646.06, YMR194W
Sequence domains: Ribosomal protein L36e
Large ribosomal subunit protein eL37A Chain: Lj
Molecule details ›
Chain: Lj
Length: 85 amino acids
Theoretical weight: 9.59 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P49166 (Residues: 2-86; Coverage: 97%)
Gene names: L9470.6, RPL35A, RPL37A, YLR185W
Sequence domains: Ribosomal protein L37e
Large ribosomal subunit protein eL38 Chain: Lk
Molecule details ›
Chain: Lk
Length: 77 amino acids
Theoretical weight: 8.71 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P49167 (Residues: 2-78; Coverage: 99%)
Gene names: L8543.2, RPL38, YLR325C
Sequence domains: Ribosomal L38e protein family
Large ribosomal subunit protein eL39 Chain: Ll
Molecule details ›
Chain: Ll
Length: 50 amino acids
Theoretical weight: 6.23 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P04650 (Residues: 2-51; Coverage: 98%)
Gene names: J0360, RPL39, RPL46, SPB2, YJL189W
Sequence domains: Ribosomal L39 protein
Large ribosomal subunit protein eL40A Chain: Lm
Molecule details ›
Chain: Lm
Length: 52 amino acids
Theoretical weight: 6.03 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P0CH08 (Residues: 77-128; Coverage: 41%)
Gene names: RPL40A, UBI1, YIL148W
Sequence domains: Ribosomal L40e family
Small ribosomal subunit protein eS32A Chain: Ln
Molecule details ›
Chain: Ln
Length: 25 amino acids
Theoretical weight: 3.35 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P0CX86 (Residues: 1-25; Coverage: 100%)
Gene names: D1290, RPL41A, RPL47A, YDL184C, YL41A
Sequence domains: Ribosomal protein L41
Large ribosomal subunit protein eL42A Chain: Lo
Molecule details ›
Chain: Lo
Length: 103 amino acids
Theoretical weight: 11.84 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P0CX27 (Residues: 2-104; Coverage: 97%)
Gene names: N1722, RPL41A, RPL42A, SCL41A, YNL162W
Sequence domains: Ribosomal protein L44
Large ribosomal subunit protein eL43A Chain: Lp
Molecule details ›
Chain: Lp
Length: 91 amino acids
Theoretical weight: 9.98 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P0CX25 (Residues: 2-92; Coverage: 99%)
Gene names: RPL43A, YP9499.02, YPR043W
Sequence domains: Ribosomal L37ae protein family
N-terminal acetyltransferase B complex catalytic subunit NAT3 Chain: A
Molecule details ›
Chain: A
Length: 195 amino acids
Theoretical weight: 22.95 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q06504 (Residues: 1-195; Coverage: 100%)
Gene names: NAT3, YPR131C
Sequence domains: Acetyltransferase (GNAT) family
N-terminal acetyltransferase B complex subunit MDM20 Chain: B
Molecule details ›
Chain: B
Length: 796 amino acids
Theoretical weight: 92.93 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q12387 (Residues: 1-796; Coverage: 100%)
Gene names: DEC1, MDM20, YOL076W
Sequence domains: N-acetyltransferase B complex (NatB) non catalytic subunit
Nascent peptide chain Chain: 8
Molecule details ›
Chain: 8
Length: 23 amino acids
Theoretical weight: 1.98 KDa
Source organism: Saccharomyces cerevisiae
5S ribosomal RNA Chain: C4
Molecule details ›
Chain: C4
Length: 121 nucleotides
Theoretical weight: 38.95 KDa
Sequence domains: 5S ribosomal RNA
5.8S ribosomal RNA Chain: C3
Molecule details ›
Chain: C3
Length: 158 nucleotides
Theoretical weight: 50.68 KDa
Sequence domains: 5.8S ribosomal RNA
25S ribosomal RNA Chain: 1
Molecule details ›
Chain: 1
Length: 3395 nucleotides
Theoretical weight: 1097.13 KDa
Sequence domains: Eukaryotic large subunit ribosomal RNA

Ligands and Environments

2 bound ligands:
Ligand MG 206 x MG
Ligand ZN 5 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.1Å
Relevant EMDB volumes: EMD-16086

Quick links

Citations

3 citation in other articles

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2 more

1 mention without citation

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Venezian et al. (2024)